What if you could visualize your specimen in true 3D at micron-scale resolution, without tissue clearing, without alignment errors, and without the resolution limits of conventional imaging?
The HREM 3D Episcopic Imaging System, developed by Indigo Scientific, represents a fundamental shift in how researchers approach 3D imaging. This is not just another upgrade. It is a new standard for capturing biological structures with clarity, precision, and context.
The Limitations of Traditional Imaging
For years, researchers have had to compromise when choosing imaging methods.
MicroCT offers whole-sample imaging, but struggles with soft tissue contrast and cannot achieve micrometer-scale resolution across large specimens. Meanwhile, Confocal Microscopy and Light-Sheet Microscopy require tissue clearing, which is time-intensive and can introduce artifacts, especially in dense or calcified tissues.
Even Histology, the gold standard for resolution, comes at a cost. Physical sectioning disrupts 3D structure, often leading to distortion, misalignment, and loss of spatial context.
The result is a persistent trade-off between resolution and anatomical integrity.
A Different Approach: High-Resolution Episcopic Microscopy
The HREM 3D Episcopic Imaging System eliminates this compromise through High-Resolution Episcopic Microscopy.
Instead of imaging thin sections individually, HREM captures images directly from the blockface of a resin-embedded specimen during automated sectioning. Each image is inherently aligned, producing perfectly registered stacks that reconstruct into accurate, distortion-free 3D volumes.
No clearing. No post-processing alignment. No loss of context.


Key Capabilities
- 1 to 8 µm isotropic voxel resolution across entire datasets
- Specimen sizes up to 25 mm, from subcellular structures to whole mouse embryos
- High contrast imaging of dense tissues and bone, without special preparation
- Enables 3D imaging of enzymatic reporters in large biological samples
- Automated sectioning down to 1 µm slice thickness
- Seamless integration with analysis platforms like Amira, Imaris, and FIJI
Applications Across Research Fields
The impact of HREM is already being felt across a wide range of disciplines.
Developmental Biology
Capture the full 3D architecture of mouse embryos with histological clarity. From whole-body phenotyping to detailed organ morphometry, HREM preserves both resolution and spatial context.
NAMS and Organoid Research
As the field moves toward New Approach Methodologies, HREM offers a powerful tool for 3D characterization of organoids and other in vitro models. Capture internal architecture, lumen formation, and cellular organization at micron-scale resolution — without sectioning artifacts or clearing-induced distortion — making HREM ideal for validating and advancing NAM-based workflows.
Neuroscience
Visualize brain structures, connectivity, and fine morphology at a level that traditional imaging modalities cannot achieve. HREM bridges the gap between macro-scale imaging and cellular detail.
Toxicology and Phenotyping
Screen structural phenotypes across cohorts with quantitative 3D morphometrics, even in dense tissues that previously required complex and time-consuming preparation.
See It in Action
Watch how the HREM 3D Episcopic Imaging System captures a complete 3D mouse embryo with exceptional clarity and detail.